Molecular recognition and self-assembly special feature: Assembly and organization processes in DNA-directed colloidal crystallization

Abstract

We present an analysis of the key steps involved in the DNA-directed assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1- versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial "random binding" phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.

Scheme 1.

DNA sequences used. AuNPs were functionalized with ≈58 ± 5 (10-nm AuNPs) or 12 ± 3 (5-nm AuNPs) strands of DNA Sequence 1, linked via a 5′ hexyl-thiol moiety. Crystals were formed via the addition of linker sequences with a 3′ end complementary to the Au-bound DNA, a single flexor base used to increase DNA strand flexibility, and a 5′ end that is either self-complementary (FCC crystals) or non-self-complementary (BCC crystals).

Fig. 1.

One-dimensional SAXS profiles of the long FCC (A) and short FCC (B) linker systems. As the DNA-AuNPs are cooled from above their melting temperature (1 °C/min), initial DNA linkages create random aggregates with no long-range order. Given time to anneal, these aggregates then reform into well-ordered crystalline domains. The vertical lines notated as 2π/Δ_Au and $\sqrt{6}$π/Δ_Au indicate the position of predicted q₀ peaks corresponding to disordered aggregates and perfect FCC crystals, respectively.

Fig. 2.

Plots demonstrating the growth of crystalline aggregates in the long FCC linker system. (A) Plot of q₀/q_0max, showing the appearance of NP scattering peaks at 54 °C and the transition to an FCC formation between 50 and 49 °C. (B) Plot of 2π/Δq₀, demonstrating the growth in nanocrystal size at temperatures <47 °C, where larger values of 2π/Δq₀ indicate larger crystalline domains.

Scheme 2.

DNA-AuNP crystal growth. (A) As the DNA-AuNPs first condense in solution, they form small amorphous aggregates with no observable crystallinity. (B) These aggregates then undergo a structural shift, forming small crystalline domains that are highly ordered at all subsequent stages of crystal growth. (C) The small colloidal crystals grow into larger crystals.

Fig. 3.

Crystal structures obtained at different temperatures. (A) SAXS pattern obtained for the 1-component (short FCC) system obtained after 5 min at 22 °C. (B) SAXS pattern of the same system as in A after combination and 5 min of annealing at 40 °C. Note that A demonstrates a more diffuse scattering pattern that is associated with a random or close-packed arrangement of particles, whereas B demonstrates a sharp FCC scattering pattern.

Fig. 4.

Plots of the progression of q₀ peak position for FCC (green trace) and BCC (blue trace) crystals. The q₀ peak position of maximally ordered crystals is assigned a value of 1.00; the shifts in peak position indicate that DNA-AuNPs designed to give FCC crystals exhibit only a slight shift in q₀ position (<1%), whereas those designed to give BCC crystals transition from a more disordered phase on a very quick time scale, but do not reach maximal order for ≈10 s.

Fig. 5.

Structural transition for 1- and 2-component systems. (A) SAXS profiles for the 1-component (short FCC) system show that early stages of crystal growth (t = 38 s; data at t < 38 s present the same pattern with broader peaks) exhibit a scattering pattern more closely resembling an HCP arrangement, whereas later stage crystals correspond to an FCC arrangement (t = 70 s). A mixture of the crystal systems is observed at intermediate time points (t = 50 s). Modeled scattering profiles for FCC and HCP crystals are shown in red and blue, respectively. (B) One-dimensional scans for the 2-component DNA-AuNP system, with an initial formation of disordered aggregates that quickly rearranges to a BCC crystal lattice. After this initial restructuring, the peaks grow in intensity and sharpen, indicating the growth of well-ordered crystals. The modeled scattering pattern for a perfect BCC crystal is shown in green.

Fig. 6.

Size and Number of DNA-AuNP Aggregates as a Function of Time. In both the 1-component (FCC) (A) and 2-component (BCC) (B) systems, there is an initial rapid drop in the number of nanoparticle aggregates (red traces) immediately after combining the solutions. This coincides with a rapid increase in the average aggregate size (blue traces). Although the 1-component system reaches maximum aggregate size in ≈5 s, the 2-component system is still increasing in size after 15 s. Note that the number of aggregates in solution is a relative value, because the cross-sectional area of the X-ray beam does not allow simultaneous probing of the entire sample.

Scheme 3.

Phases of early stage crystal growth. Initial nanoparticle aggregates are small and form quickly (phase 1). After forming, these small clusters then rearrange to a crystalline formation and begin to coalesce into large aggregates with multiple discrete crystalline domains (phase 2). After formation of large aggregates, these small domains slowly reorient to form a large DNA-AuNP crystal (phase 3). The data presented in Scheme 2 represent growth phases 1 and 3, because phase 2 occurred on a time scale unobservable with the previous experimental setup.